Hi gromacs users,
I am working on protein-ligand simulation..The commands were given in the
following order
(1)
source leaprc.ff14SB
loadAmberParams frcmod.tip4pew
loadAmberParams frcmod.ionsjc_tip4pew
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec_final.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
receptor = loadPDB rec_final.pdb
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvateBox complex TIP4PBOX 10.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb
quit
(2)
acpype -p com_solvated.top -x com_solvated.crd -b complex
After the following grompp command,
(3)
gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em
where
#em.mdp
; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em
#Grompp minimization
integrator = steep
nsteps = 500
nstlist = 10
energy-grps = receptor LIG
cutoff-scheme = verlet
vdw-type = cut-off
rvdw = 1.0
coulombtype = pme
rcoulomb = 1.0
The fatal error was
(1) Group receptor referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index groupnames,
in which case you must supply an index file to the '-n' option
of grompp.
and
NOTE 1 [file complex_GMX.top, line 77775]:
System has non-zero total charge: -0.000243
Total charge should normally be an integer.
How can I fix the error? What commands should be given? Please help.
The protein was rec.pdb and ligand was lig.mol2
Where to spot the names in the .GRO file for energy-grps
Thanks,
Subashini.K
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
